Equestria and the Time Lord Episode 10: The White Plague
by The Orwellian Writer
Summary: The Doctor and his new companions arrive on the Carrier 9 viral research vessel, quickly finding that it is infested with a deadly plague that eats away at several parts of the body, with only one pony having the means to hold it back. As his companions contract the disease, The Doctor discovers what the pony has been keeping from his patients. But this disease may kill them first.
1. Prologue: Escape to Danger

Equestria and the Time Lord Episode 10: The White Plaque

Prologue: Escape to Danger

**=The Carrier 9, Docking Bay 1, 3222 C.E. =**

Trixie and Puzzlehunt stared with feigned boredom at their new surroundings. But really, they were in awe at the land around them. It wasn't very impressive to the Doctor, though. The place was gray and dirty, not very nice. It was a large room, and in the place of one of the walls was a window with a glow surrounding it. Behind the TARDIS were about 12 entrances to escape pods lining the walls next to them. Besides that, the room was empty. They were alone.

They looked out the window. "Well you've certainly brought us somewhere, but I'm dubious as to whether or not we've actually traveled in time." Puzzlehunt said cynically.

"No, I'm pretty sure we're in a different time period this time around." The Doctor said. "Do you want to see where we are? I rather want to look around."

"I suppose I'll allow that. This place seems to be somewhat unimpressive though." Trixie said.

The Doctor knew they were lying, but didn't say anything about it for now. He just smirked and walked toward the exit to the room, which he guessed was a docking bay. Wait a minute, he thought. If it was a docking bay, why was the place so completely empty?

And they walked to the door an out of the docking bay, and into whatever was out beyond the door.

And it was just a hallway. The Doctor had grown a bit tired of hallways by now. There wasn't even anything interesting about this hallway. It appeared to be a light gray color with the pattern of stone, and it was well lit so the color wouldn't make the corridor seem depressing, in which it failed.

Another thing about it was that there were no sounds. So quiet it was eerie simply because there weren't any engine sounds that gave you any hint that there was something alive on this ship (which, from experience, there certainly was.) yet the lights didn't seem to be nonfunctional in anyway. Maybe the engines didn't give off any sound.

And then they heard something. There was somebody coughing somewhere. And there appeared to be a large smear of blood covering a part of the wall with green bubbling in it. And they refused to look at the old body at the bottom of the smear.

"I'm starting to miss the quiet." Puzzlehunt said to himself.

"Wow, really? How inquisitive. I never would've thought of that." Trixie said sarcastically.

Puzzlehunt rolled his eyes as they continued walking through the corridor.

The corridor was mercifully short. A few steps away from the body, they came to a door. And so, they went through it (Although they didn't really have another choice at the moment) and went into the room on the other side.

It was a large room with the walls decorated the same way. There was another large window lining one whole wall, although this looked into a chamber. And in that chamber was a stallion lying on his side, and he was the source of the coughing they had heard earlier.

And another stallion walked into the room. He was very odd looking. He has a white coat, a ragged white mane, pale eyes that were nearly white, sunken facial features, and around most of his body was a white harness with wires coming from the door he had just walked through. He walked over to the chamber, not noticing them standing there as he pressed a button on the wall. "You need to stand up." He said to the stallion in the chamber.

And slowly and groggily, although the Doctor would never know how, the stallion managed to stand up. Based on how deteriorated the stallion's body looked, The Doctor was sure that he had some kind of plaque. He looked very similar to the stallion that had just walked into the room. His coat and mane were slightly more colorful though.

"Now, everything appears to be in place. We will administer the first test immediately." The white stallion said.

"Mystery was all black. This one is all white. Can't we get a little more diversity here?" Puzzlehunt asked sarcastically.

The white stallion didn't appear to hear them. "I'm setting the proper settings." He said to himself. The communicators weren't engaged, so the stallion in the chamber didn't hear anything he said except the first sentence.

And whatever the experiment was, whatever they were testing, began at that moment. The white stallion quickly put on goggles.

They all watched as a white gas seemed to make the image in the chamber slightly more fogged. It became harder to see the stallion in the chamber, but you could tell what he was doing. He coughed profusely on the white gas for a tense minute.

And then he stopped coughing on it. In fact, it looked like he was finding it difficult to breathe at all. He tried to take breaths, but they didn't seem to absorb enough. He continued his attempts, but his lungs wouldn't accept the white gas into his body, and he seemed terrified by it. Obviously whatever he expected the experiment to be about, this was not it at all, and he ran around, trying to make his lungs breathe in, but they wouldn't do it.

And in one second, it happened. The white gas turned into a white flash that stayed for only a split second before subsiding. They stallion collapsed. He was dead, nearly charred to the bone. The white vapor was gone without any trace, and you could see the grim sight crystal clear.

The stallion's body slid slightly, leaving a small smear of blood across the floor. The sight was indistinguishable from the body that was in the hallway.

There were even small green bubbles rising in the small growing pool of blood. But they soon all popped, and the blood was a pure grim red.

The Doctor, Puzzlehunt, and Trixie all watched in shock, still nearly blinded from the white flash, although that was wearing off now.

The white stallion took off his goggles. He craned his neck forward. From his position, he examined the body quite closely. And when he saw the color of the blood, he gave a very satisfied grin that only he understood. "And it works perfectly." He mused to himself as he left the dead body behind impassively, without a care as to the living being it had been originally.


	2. Chapter 1: The Centre

Chapter 1: The Centre

**=Carrier 9 Viral Research Center, The Cure Administration Testing Site, 3222 C.E. =**

"Well, that was rather unexpected." The Doctor whispered to his companions. "Now we have two options. One, we go back to the TARDIS and leave immediately. Or two, we walk up to him and talk to him, giving away our presence immediately and taking away any and all chance of getting out of this situation."

Before Puzzlehunt and Trixie had any time to answer, The Doctor chose the second one. He walked over to the white stallion nonchalantly. "Hello."

Puzzlehunt and Trixie groaned quietly as he began to back out of the room as quickly and quietly as they could before…

The stallion shot his head in their direction, now being able to see all of them. His eyes widened so it was impossible not to see the malevolence the stallion was now gearing right at them.

"What are you doing here." He said in a dangerous calm voice.

"Well, we landed here by accident, and we were now just looking around before we left." The Doctor said.

"You've landed into the wrong place." The stallion said, his air of calm beginning to break.

"Really? What's wrong with this place?" The Doctor said, having a very good idea what was wrong with this place.

"You have made a tragic error in judgment, coming onto this ship, you know. This ship, for a very long time now, has been infested with a deadly plaque. And all the contractors have been quarantined. All potential contractors will be quarantined. And now, it appears you will have to be quarantined. Which means, of course, you will never be able to leave." The white stallion said, bridging in between calm and insanity.

"Never?" The Doctor asked. "We will never be able to leave?" He looked over to Puzzlehunt and Trixie, who did not seem very pleased at the concept. "That doesn't sound like a very promising idea."

"Well, I'm afraid you have no choice in the matter. We wouldn't want a microbe of this disease returning to Gaia, now would we?" The white stallion asked simply.

"No, that wouldn't be very good." The Doctor said. "Tell you what, would you like any help with the curing of this disease. We did bring several medicinal supplies aboard our ship, and the door is unlocked." He didn't seem worried at all that he had just said that. Puzzlehunt and Trixie did.

It was then that the stallion smiled at them. "I'll tell you what, I'll get your supplies for you. And you know what you can do for me?" And despite his nimble form, within seconds he had Puzzlehunt and Trixie unconscious and was leading them along to quarantine.

**=Carrier 9 Viral Research Vessel, The Quarantine Section, The Designated 442 Bunks, 3222 C.E. =**

When Trixie woke up, she didn't know what hit her. All she knew was that she was lying on the top of a bunk bed, and her head was seriously spinning. She pulled herself up. She looked down in the bottom bunk. Puzzlehunt was lying there. And what the Doctor was doing was pacing the floor in front of the beds.

"Oh, you're awake too." He said, noticing her. "Okay, so that stallion is going to get some medicine from the TARDIS, and then he's going to retrieve us."

"Do you actually believe that?" Trixie asked.

"Not for a second, but there's always the chance that he will do it, and that's all we have to hope for in this closet sized room." He said, looking around.

"Thanks for successfully getting us into another mess, Doctor." Puzzlehunt said.

"This is only our first actual trip!" The Doctor said.

"And you've walked us right into the center of a plaque ship. With a deadly plaque. That could kill us. Did you consider that?" Puzzlehunt asked.

"It's not going to kill us." The Doctor said.

Puzzlehunt relaxed a little.

"At least not right away, anyway."

Puzzlehunt and Trixie glared at him, and then sighed. "We're stuck in quarantine. We've been left to die here, and the only thing they're going to do to acknowledge is lean the blood off the sheets and give them to somepony else." Trixie said.

The Doctor decided not to tell them about the bodies that had been stuffed in the corner, and simply tried to not inhale.

"So what are we going to do? Wait for somepony who may never ever come? And if he doesn't, we'll inhale a disease and gradually fall down dead. That's no good. We need to do something different, but from what I can see, there are no exits from this room. So all we can do is wait for somepony who might never ever come, leaving us right back where we started." Puzzlehunt explained as he stopped talking in some kind of miracle of nature.

"We might be let out. You're not putting enough hope in this." The Doctor said in a cheerful tone.

He received two more glares as a result of his cheer. "Okay then."

And they sat there, not knowing anything that was going to happen next. Really, if the stallion actually was coming to help them and get them out of quarantine, he was sure taking his sweet time with it. The Doctor just stood there. You could tell he was obviously thinking about something important.

Anyway, Puzzlehunt and Trixie were basically rolling their eyes at his determination, having none of it themselves.

"Hello there." The white stallion said nonchalantly as he walked back into the room, carrying tons of vials.

This certainly surprised Puzzlehunt and Trixie quite a bit, making them jump a little.

"I went into your ship and I got the medical supplies you spoke of." The white stallion said, obviously not surprised in the least at what he had seen in the interior of the TARDIS. "One of you will help me develop these chemicals and the others, and the other two will work on checking the patients, a job that had solely fallen on me before."

The Doctor stood up. "I'm supposing it's me you want to come with you, correct?" He walked over the white stallion, waved to Puzzlehunt and Trixie, and then they walked out the door.

Puzzlehunt and Trixie stared at the now closed door in horror. "Please tell me he didn't-" But the sentence was cut short as the doors on either side of them slid right open.

There were rows upon rows of horribly ill and vomiting ponies in front of them. They looked like the stallion who had been in the chamber. They all had a deadly plaque, and now they had been exposed.


	3. Chapter 2: The Plague

Chapter 2: The Plague

**=Carrier 9 Viral Research Vessel, The Quarantine Area, The Designated 422 Bunks, 3222 C.E. =**

For 10 seconds, Puzzlehunt and Trixie thought they were already dying. And then, the door snapped shut.

The voice of the white stallion, although sounding much healthier than it did now, came over the loud speakers in the room. "Now that you have seen an active demonstration of what this plague does, I'll explain its stages. First, within seconds, you feel a perpetual throbbing in you flank."Puzzlehunt and Trixie realized with horror that they could already feel the throbbing pain directly where the tape had said.

"Next, over a very slow period, our cutie mark is eaten away at and disappears, leaving only scarring in its place."

Trixie never told anypony, but she was very nearly sick.

"Then, you feel an incredibly faint feeling moving through your body, and it is difficult to stay conscious."

Puzzlehunt, although he was later certain it was just his paranoia, felt a faint cold shiver go down his spine.

"This period ends when the disease stops at your brain. With that, you begin to lose you memories, in the most painful stage of all. Your memories begin to deteriorate from the present backwards. Through it all, body fat and muscle burns away."

Trixie looked around, her blood going cold as she focused on the pain she was feeling, and realizing what it truly meant.

"Through a painful process, your memories vanish totally and all mental functions shut down. I will give you a word of warning now. This disease does not kill you. You become like a zombie, but with even less life than that. Not dead, but almost, and certainly not alive. I often think of it as being worse, but I never cared. Your body can be switched on and off to be contorted until it is almost unrecognizable by the disease. Usually, in fact, it will be unrecognizable. You will not be switched off again by now. Your mind was given up a long time ago and your body has followed, and the thing that has replaced you will only live a few hours before it dissolves."

This time, Trixie really was sick, and Puzzlehunt came close.

"You have now been exposed to the disease. It is festering in your body. And now you have to make sure all the others that have the disease are monitored. You will work continuously until you reach the final stage of the disease. But don't worry, I'll make certain you are dead a long time before then." And the tape ended.

The doors slid open again.

**=Carrier 9 Viral Research Vessel, The Viral Processing Laboratory, 3222 C.E. =**

"What do you want us to do?" the Doctor asked.

"I have taken all the medicine you spoke of from your ship. Interesting interior. We will, no, I will, process it to see if it kills the disease." The white stallion said.

"What do you want me to do?" The Doctor asked.

"You will help me rebuild the harness." The white stallion said, gesturing to the harness he wore around his body, with the wires running from it through the door.

"Why so?" The Doctor asked.

"Through a blend of mechanical and chemical, it allows the disease in my body to stop affecting me. It has erased most of the functions that the disease attacks and provides it artificially." The white stallion said.

"But that leaves you not alive, but more undead." The Doctor said. "How do I do it?"

"All the scientists who understood its design died before the could make more than one. I was coherent enough to keep the chemicals that keep me alive supplied, but I do not understand it myself." The white stallion said.

"And you expect I will?" The Doctor asked.

"Indeed I do." The white stallion told him, shrugging.

"How?" The Doctor said, wondering if there was more to learn.

"I'm sure you'll figure something out. You haven't been infected yet. There's nothing holding you back from that work. What's left of the first designs is in that room." The white stallion said calmly, pointing to the door on the far side of the room.

"And can I have a sample of the chemical you need to finish it?" The Doctor said.

The stallion threw it into his hands. It was a jar of some white liquid.

"And before you asked, I already tried. It doesn't help anypony without the support of the harness. It might even make it worse."

The Doctor nodded and slowly made his way to the door. He looked at all the glass cylinders that formed columns through the room. He realized that the ship must study extraterrestrial forms of life, and they had picked up the disease on the ship by accident. These cylinders that had fallen into obscurity were all the others they had found, the one they didn't care about anymore.

The Doctor looked at them in fascination, but continued walking. He slowly made his way to the door, opening it. He wondered about how things seemed to go wrong at places so quickly it was hard to imagine when things were right there. Naturally, he always ended up at those places.

He opened the door and went into the room. It was obvious that even though the white stallion knew what was in here, he hadn't come to look at it for a very long time. Of course, nobody knew how long the plaque had even been there.

He looked at the crude unfinished machinery lying on the table in front of him covered in dust, and looked at the parts he had been given to finish it, also covered in dust. He started by cautiously wiping the dust off of what remained of the second harness, and then the spare parts. He checked over to make sure they hadn't decayed beyond being able to use them. That was very important.

He looked around at the stone patterned walls, and thought of how the lighting of this place wasn't going to work for him. The lights were dim from lack of use, and he rather wanted to find a light switch somewhere in the place so he could see what he was doing better.

Ignoring the bubbling blood stains he saw around him, he began to look through the room. He didn't find much, and it was a big room. He noticed what he was looking for.

Unfortunately, there was a body at the floor next to the light switch, and the light switch itself was smeared in infected blood.

He sighed, wondering how he was going to get some light. He then remembered something obvious, leading him to slap his forehead. He pulled out his sonic screwdriver, and after using it for a few moments, the lights slowly glowed bright enough.

And then he saw it, and he never would have noticed it if he hadn't turned the lights back on. It was up to him to decide if it was a good thing he had done so or not.

Standing in one of the puddles of blood, there was something in the room with him.


	4. Chapter 3: The Invisible Enemy

Chapter 3: The Invisible Enemy

**=The Carrier 9 Viral Research Vessel, Quarantine Area, Section 1, 3222 C.E. =**

Puzzlehunt and Trixie used their magic to pull two pieces of machinery off the wall. And of course, they didn't know anything at all about how to use them.

"These are the medical scanners, in case you didn't know." Said the recording. "You press the button, and then wave the red light that comes out of them over the patient. It then gives you a diagnosis of which stage they are in. Your job is to notify me immediately of any of them nearing the final stage."

"Thanks a lot." Puzzlehunt said sarcastically.

"You're welcome."

It was then that they realized that it wasn't the recording. They turned to see that the white stallion was in the room with them, grinning at them. "Move along."

**=The Carrier 9 Viral Research Vessel, The Chemical Testing Laboratory, The Mechanical Construction Lab, 3222 C.E. =**

The Doctor looked at the disturbing figure in front of him. It was equine in basic form, but every single part of its body was swollen. Its body was a dark green in some areas, but mostly it was pus yellow. It had hair sprouting out in random areas of its distorted flesh. One of its eyes was completely a yellow green color, and the other looked like a normal eye. This eye, however, was black and extremely dilated, making it difficult to see the white. The thing seemed to be gushing blood from several small purple spots on his legs.

And then it stepped forward at him. As it walked, it made its trail of blood follow along with it. The Doctor realized another detail. Two of it hooves were fused together slightly, making it difficult for it to walk very quickly.

Then it tripped over, lying in its own blood. And slowly, the body of the thing began to split open, spilling a flood of mutated blood onto the floor until that was the only part that remained of the creature that had been mutated by the disease.

He looked over the floor, seeing how few of it was safe to walk on. He began to hobble around the puddles until he was over by the table. He grabbed all the spare harnesses, deciding that was no longer any good reason to be in this room. He walked out. This didn't happen to him often, but the display of gore he had just seen made him rather sick.

He left the room, and discovered the white stallion had left. Apparently he had left a letter of some sort. It read,

_I've decided to check on your friends' progress. I want to make sure that being exposed to the disease has given them a proper work incentive for them. Carry on as you are, and you may be able to save them before death._

He didn't bother to leave a signature.

The Doctor realized the repercussions of the last line on the letter. He knew that in his own moral code, he had no choice. So he continued on working like he had been told, as he knew that saving his friends was the most important thing right now.

**=The Carrier 9 Research Vessel, The Quarantined Area, Section 1, 3222 C.E. =**

And the white stallion, after he had shown up, didn't interact with them again. He didn't even watch for long periods of time. For the most part, he just vanished, but they knew that he was still there, waiting for a moment to check up on them ad project fear into them to make them keep going on like his until they died and had their bodies destroyed, unceremoniously, and with no consideration to who they were. Patients, and that was all that was any matter to the white stallion.

And that was something that Trixie found rather terrifying. She shrugged it off and continued, ignoring the continually worsening effects of stage one. She looked down. Her cutie mark was still there. She sighed and scanned another pony, thinking of how she was pounding more of the disease into her body continually. She could feel that one of her hooves had gone completely numb by now.

Then, one of the ponies she was about to scan woke up and looked at her. She wasn't actually aware that you could do that by the stage she looked to be in. he pony that had woken up, a mare, seemed dizzy and uncoordinated, having yet to collect her bearings and realize where she was.

Trixie wasn't a good conversationalist, but she realized that she was going to have to talk to this mare now so she didn't panic or something even worse than that.

She gave a fake smile, knowing there was nothing to smile about around here, not with the plaque running rampant. "Hello." She said as politely as she could.

The voice actually seemed to startle the mare in the bed quite decently as she looked up at her, unable to say anything that made any sense. After a while, she successfully gasped out, "Hello."

"What's your name?" Trixie asked awkwardly.

She didn't reply to that one, and seemed to strain herself for the answer.

"How are you feeling?" Trixie asked, deciding not to dwell on it.

"Not very well." She admitted simply.

"Well, I'm not really a doctor, but I'm still dong what I can." Trixie said, much nicer than she would be to anypony healthy.

"Well, thank you for that anyway. I'm not sure why I'm getting all this fuss though." She said, rather confused.

"Why's that?" Trixie asked, at quite a loss for why the mare wouldn't know.

"Well he last thing I remember before I woke up now, was that bleach white stallion assuring us that our disease was nothing serious. We'd just unleashed a minor flu." The mare explained.

Trixie tensed up. So the white stallion lied. Told people something assuring that they didn't deserve to be lied to about. She would dwell on that later, when it was important.

She didn't have until later. The repercussions came right that minute.

A gun was aimed at her back she froze and fear as the white stallion walked around her with chilling agility. Then, without missing a beat, she knocked the mare unconscious again.

Then he drew out a vial of a purple liquid.

"You found out something you weren't supposed to." The white stallion said. "There will be punishments for that.

He injected the mare twice. She coughed up blood for a minute, and then quickly fell back unconscious.

"For example, now that you know about the cold secret, you might as well know now that before anypony reaches the final stage, the most deadly of all, they are injected with a poison that, like the disinfectant system, is completely deadly, but eliminates the disease in the body. Just thought you'd like to know. Oh, and if a pony is injected at stage 1, the disease just goes faster."

And in seconds, he had forced her down to the ground. As he held her down, they didn't notice anypony watching. It didn't matter now. He took the vial and injected Trixie twice in the leg, standing back and leaving her there.

Then he left.


	5. Chapter 4: Terminus

Chapter 4: Terminus

**=The Carrier 9 Viral Research Vessel, The Virus and Disease Processing Laboratory, 3222 C.E. =**

The process of creating the harness to hold back the disease seemed pretty simple to do. The incomplete wiring wasn't all that difficult to fill in and complete, and The Doctor had actually completed one of them in only a few minutes. But this was the only one that was partially complete, while all the others hadn't been started, and the plans for them were gone. So The Doctor was left to start from scratch.

The white stallion walked into the room and looked at the completed harness, but did not smile. "Well done."

"So what's this about lying to your patients about the nature of the disease?" The Doctor asked swiftly.

The white stallion gave him a very brief look of genuine horror. "What are you talking about?"

"Someone pushed a call button, and I heard everything that was going on in the Quarantine Area. Then I heard something about you poisoning anyone who got too close to death, and then a struggle. Now I'm going to hear the part where you deny everything." The Doctor said coolly.

"I don't know what you're-" There was a brief pause as the white stallion registered what the Doctor had just said. He sighed. "How very clever of you. Yes, I know exactly what you're talking about. And it appears that we have reached an impasse. I can't kill you, because you're the only one who can help me. You cannot harm me, because I feel no pain. The effects of the harness make me nearly, for all intents and purposes, dead. My body has stopped and my life processes are supplied artificially to hold the disease in place. In spite of this…"

The doors all closed and locked.

"No one will leave this room."

**=The Carrier 9 Viral Research Vessel, The Quarantined Area, Section 1, 3222 C.E. =**

Puzzlehunt removed his hoof from the call button and ran over to Trixie, who did not look good at all. He lifted her up with magic onto one of the empty beds, looking at her with shock. He had utterly no idea what to do at all. He pressed the call button again, but found it did not work. Then he realized there was only one potential alternative left if he couldn't help Trixie and he couldn't help the Doctor, and it wasn't a very complex one: He had to get out of Quarantine now.

The only problem was that the doors were nonexistent, and the walls were 10 feet thick out of an incredibly magic resistant material. There was no way out.

Still, from what the white stallion had said, Trixie didn't have long, and although he was arrogant and pompous, he didn't really want her to die, not out of love or even like, but something.

And he ran through the area, looking for just one door that he could escape from. The Quarantine area was very large, but there has to be one. He had seen the white stallion walk out of it himself. And so that's where he ran to. That's where he went. And that's where it was. A door that was the same distance thick and the same material, but it was the best bet he could think of. And so he aimed his horn at the one place he thought he could possibly penetrate the door. He went for the edge of the door. He aimed into the tumblers. And after he focused for what seemed like several ages on that part. The door slowly slid open like it was opening the end of the world out into the world.

And he walked out into this world.

**=The Carrier 9 Viral Research Vessel, The Disease Processing Laboratory, 3222 C.E. =**

The Doctor and the white stallion sat across the table rebuilding another harness.

"So why do you want these harnesses to be built?" The Doctor asked as he connected two wires.

"To be honest, I don't." The white stallion said.

"Then why are we doing it now?" the Doctor asked, having an idea of the answer.

"Because I'd rather be doing something than standing in the Quarantine area, watching everyone around me die when I won't due to something I can't take off anymore."

"That makes no sense to me. There are plenty of other things to be doing besides something you don't want done." The Doctor said.

"Would you rather I take a knife and go on a murdering spree?"

"I meant something different. Weren't you processing those medicines?" The Doctor asked.

"No point. I occasionally lapse into moments where I forget that there is nothing I can do to help them."

"Why is that?"

"Because it's gone beyond anything you can control."

"So you've given up. But from what you imply, you were quite desperate to help them not long ago."

"That would be correct. I remember the day this ship first went off into space to document to other organisms in the universe. I was pretty high up in rank. The captain of the ship, in fact. I wasn't too connected to my scientists, which was perhaps my main flaw. My coat has always been white, but my hair was once yellow. I used to be a Pegasus. But in order to don this harness, which has since fused with my skin, my wings had to be severed. The ship was illegal and there weren't as many crewmembers as we had hoped for." The white stallion said, looking slightly happy and slightly angered. He seemed just happy enough to give a slight smile.

"Illegal?" The Doctor asked, wanting confirmation.

"Princess Celestia claimed that the planet was not ready for the advances we might find, while the rest of the government wanted to shut us down because we might bring a disease back with us. They would not give us authorization to launch the ship. We launched anyway.

"And you are bringing a disease back with you." The Doctor said.

"This is why I am never bringing us back." The white stallion said. "We will never return to Gaia. I will live my existence out here, as I can no longer call it life."

"Really? Going back a bit, why is the cure out of your control?" The Doctor asked, knowing why.

"Because I have given up." The white stallion said as he gave The Doctor a grim look, frantically connecting wires together.

"Leaving your whole crew to suffer that disease? That's a rather evil thing to do." The Doctor said, wondering if he could strike a nerve.

"Princess Celestia was holding back her kind from any advancement that tried to get through. Outright Manipulation and evil from behind the scenes, that is the greater of the evils. The kind you will never know. The kind that everyone gives in to."

"But that's what you are." The Doctor said.

He struck a nerve.

"Do you know why I lie? Mental pain exceeds physical in every respect. If they lived knowing they were going to die, that would make life worse than the disease." The white stallion said, his voice almost a shout. "That is why I lie. And now all pain will cease, because I have made my decision. This ship will be sterilized. I am putting it on self destruct!"


	6. Chapter 5: Trap of Steel

Chapter 5: Trap of Steel

**=The Carrier 9 Viral Research Vessel, The Disease Processing Laboratory, 3222 C.E. =**

The Doctor looked at the white stallion from his position across the table. "I see. We've reached that point of time where rationality dies off completely, correct?"

"I am not irrational! This ship is past being saved. Even if we find the cure, the whole ship doesn't work anymore. Everything on it is infected. And there's no place to go, because then we'd bring it there! I can't save this place anymore!" The white stallion yelled as he lost rationality completely.

"I see." The Doctor repeated. "Can I have the TARDIS medicines back then?" he began to put them back into his pocket.

"NO! Stop it! Now that you've come so close to this disease, you can never leave! You'll just bring it with you! And besides, you'd leave your friends to die away here!" The white stallion said.

"Not so. Could probably help them if I brought them back to the TARDIS." The Doctor said, taking all his stuff as he stood up.

"You can't go anywhere! I will not allow you to go back to Equestria. I will not allow you to go anywhere! You will not bring this disease out of this ship! I will kill us all before I allow that!" The white stallion yelled, his voice breaking.

"Yes, Rational thought, in your case, is most definitely a thing of the past." The Doctor said as he sighed and pulled out his sonic screwdriver.

"Cease doing that! You cannot leave! You have to stay here!" The white stallion said as he went through a large bout of temporary insanity.

"Really?" The Doctor asked simply as he pressed the button on the sonic screwdriver. It whirred for a moment, and then the doors all slid open simultaneously. He then grinned and walked toward the door.

It was then that the white stallion took a turn for the very violent. He grabbed a glass rod that was used for testing in the lab, and ran over to the Doctor.

He then smashed it over his back.

The Doctor screamed for a moment and then fell to the ground. Luckily, he wasn't cut and was still conscious, so he began to get back up again.

The white stallion then tried to stab him with the broken end. But then all of a sudden, he stopped breathing completely.

The Doctor looked to see that the wire connected to his harness was being burned away as it burned in two completely. The white stallion fell inert, looking to be almost dead, if not completely dead.

Puzzlehunt was standing in the doorway, destroying the cable with a magic bolt. When it was done, he disengaged the spell and walked over to the Doctor.

"Even if he didn't just die now…you still killed him." The Doctor said to him.

"I'm certain that he deserves it. Trixie is still in Quarantine. I'll get her. She really needs help." Puzzlehunt said simply.

And he ran out the door, and The Doctor walked after him as quickly as he could.

Meanwhile, the white stallion was having quite the experience. All his body parts seemed to be coming back to life, but some looked as if they might fail. And it didn't help that now the disease in his body was active again. In fact, it looked like he probably would lose the internal battle. His heart came back into proper working order, and so did his lungs.

He could breathe again, and his heart began to pump blood again to the other regions of his body. He could not pull himself to his feet as the disease attacked his functioning organs. He gasped wildly, but that didn't give him enough air.

And then he was okay. The disease just stopped. The white stallion realized in shock that his harness, which still had minor functions before it gave out, was able to compress the disease into one organ he could live without and shut it down.

And so he cut it out himself.

**=The Carrier 9 Viral Research Vessel, The Hallways Outside the Quarantine Area, 3222 C.E. =**

The Doctor looked at Trixie as Puzzlehunt set her down. She didn't seem very good. She had left Stage 1 and her cutie mark had vanished completely.

And they took her back to the TARDIS. She lasted that long. They were able to take her into a small room, the same place The Doctor had made Puzzlehunt a natural unicorn. And so they were able to strap her down.

"Okay lets think about this." The Doctor said. "A cutie mark, from what I gather, is a series of chemicals that arrange themselves based on unconscious mental gathering."

Puzzlehunt followed along as best he could.

"So perhaps this disease isn't a disease, but a poison. A chemical that reacts poorly to the chemicals in your body. That's why the whole ship is infected. It's in the blood." The Doctor said.

"So how did we get it?" Puzzlehunt asked. "We never touched any blood."

"Perhaps you inhaled the fumes from it. That's the only likely possibility." The Doctor said. "That's why they couldn't cure it here. They were working from a false start. Chemical poisoning is much easier to treat than a new disease."

"So how did they pick it up if they were studying new diseases?" Puzzlehunt asked.

"I'm working that one out, but I believe that it is a compound created from the very fluids that are being used to cure the white stallion. The scientists worked out what was going on, but they didn't have the opportunity to tell the captain, who is the white stallion, before they died." The Doctor said. "The poison she was injected with is in fact the same stuff dyed purple so nopony would make the connection. The white stallion already knew the fluid would be harmful without the harness, but he never knew why."

"So what happens now?" Puzzlehunt asked.

"We have to get a sample of it if we want to cure it." The Doctor said. "So we can't just leave. But now the white stallion is completely determined to blow up the ship, so we have a time limit."

"Isn't there always?" Puzzlehunt sighed.

"What do I do?" Trixie said weakly. "I know that there is one important thing I can do from here."

"What would that be?" Puzzlehunt asked as he rolled his eyes, guessing the answer.

"I can be here to give you something to work towards. I'm certainly worth the trouble." Trixie said as she gave an arrogant smile.

Puzzlehunt rolled his eyes as they ran out of the room.

**=The Carrier 9 Viral Research Vessel, The Bridge, 3222 C.E. =**

The white stallion could feel the disease (or so he thought of it) starting in his body from Stage 1. It would be an odd process, and he knew he would have to slice this harness off if he wanted to survive. The thing is that he didn't want to.

He looked at the limestone patterned walls and reached for the sterilization button. But then there was a buzzing red light on the console. His eyes widened when he realized there was only one person that could be calling him.

He pressed the button.

"You are charged with crimes of launching an unauthorized vessel. You will bring the vessel back to Equestria to stand trial immediately." Said a firm female voice that got right to the point.

"So you've found me this far away. I'm afraid this ship has contracted something and we cannot return to Equestria." The white stallion said,

"If you do not come then we will take you by force." And then the ship began to turn seemingly by itself.

"You do not know what you're doing. If you bring this ship back, you'll poison Equestria!" The white stallion yelled.

But there was no answer as the ship kept accelerating uncontrollably.


	7. Chapter 6: Survival

Chapter 6: Survival

**=The Carrier 9 Viral Research Vessel, The Bridge, 3222 C.E. =**

"Why are you doing this?" The white stallion said, regaining calm.

"You were not to launch this ship. Equestria cannot know it exists. We will teleport on board and then apprehend you." The administrator said.

"Really?" The white stallion said. "I'm not the one that needs to be apprehended. If you had a clue what was going on onboard this ship, which you don't, you wouldn't dare come near us. You would decide that you would blast this ship out of the sky with all of us in it, which I want anyway. But like the ponies who live under you, you refuse to get it. You refuse to understand. But don't say that it wasn't me who warned you about this. You knew beforehand, but you didn't wish to believe it."

And he jammed his hoof down on the sterilization button.

It began to glow a brilliant white, but then stopped after ten seconds. "You idiot! You're ship is hardly stable! It's taking ten of us to halt your ship's systems! We are going to get you immediately!" The administrator yelled through the communicator.

"Really?" The white stallion said. "You won't want to do that. But then, you don't care what I say…yet."

And seven ponies teleported into the middle of the room. Six were Royal Guards and one was the administrator. The administrator was a light brown coated mare with a light purple mane. "All right. We've come. Get over here."

"Really? That's the best you can do? That's the best thing you can say to get me to go over there?" The white stallion said. "That isn't enough for me."

All the Royal Guards aimed their horns at him. The administrator walked over to him. "Must we do this? We'll take you by force. You don't get an option." She said.

The white stallion looked at her as she backed him into the control panel. "Yes I do." And he pressed the sterilization button again.

There was a crack over it as a white light flooded the room. When it passed, the white stallion was safe due to his body being immune to the disease and the sterilization procedure was also based on the chemical that was still only partially in his body.

But the Royal Guards and the administrator were now only charred bodies in burnt up armor.

The white stallion looked at this. He had just made the ship ready to burst. There would be energy blasts all over the ship, and if the unicorns holding the ship in place slipped, it would all come apart.

Okay, he would have to wait until they slipped their grip. Then the disease would be wiped out. Then they would all truly be safe.

**=The Carrier 9 Viral Research Vessel, The Docking Bay, 3222 C.E. =**

The Doctor and Puzzlehunt slowly walked out of the TARDIS, heading the way they went originally to the disease processing lab. They didn't know about the ship being recently destabilized, but it wouldn't be that hard to figure out.

So they walked out of the docking bay and began to run, knowing they wouldn't have much time anyway. And they ran through the same halls that they had been walking through when they first arrived. They passed by he body that had given them their slight first amount of knowledge about the disease on this ship.

And then they walked into the room where they had seen the white stallion testing a more efficient way of killing all the ponies who were infected. But there was something quite different about that.

There were some dangerous white sparking coming from both inside the large booth and from the control panel. Taking a moment's pause, the Doctor walked up to it.

"Well this doesn't seem to be right." He said as he examined it.

"Really? Wouldn't have noticed that." Puzzlehunt said sarcastically.

The Doctor didn't acknowledge him as he looked at the sparks more closely. "I think that the white stallion was attempting to blow up the ship by releasing a large sterilization wave from here. But something made it unstable."

"Well, I was worried nothing good was going to happen to us." Puzzlehunt said, rolling his eyes.

"Time limits always seem to bring out the best work, don't you agree?" The Doctor asked as he walked out of the room cheerfully.

Puzzlehunt could really just not believe the Doctor sometimes, and they hadn't even known each other that long.

He sighed as he followed after him.

But beyond that room, it was rather dark, giving the stone patterned walls a more sinister feeling. It was also that this was the area of the ship that was most encased in infected blood all over the place. It was sickening because if you stepped in it, you'd get infected when the chemicals in it seeped into your skin.

It was then that Puzzlehunt realized with a shock that he had completely forgotten that he was already infected himself. He was still in stage one strangely enough. Maybe he was walking around enough that he was partially fighting it back.

And suddenly he had an idea. Unfortunately, he didn't have the resources to put it into action. He saw the Doctor walking into a room in front of him.

And he began running toward him.

**=The Carrier 9 Viral Research Vessel, The Docking Bay, The TARDIS, The TARDIS Medical Facility, 3222 C.E. =**

Trixie slowly rose out of unconsciousness, thinking about how often this happened to her in only the last two days.

She noticed that she was back in the Doctor's ship (The TARDIS, she believed) and there was a tube stuck in her mouth. Naturally she panicked and tried to jump up, but found that her hooves were strapped down to the table she was lying on.

The disease in her…she could still feel it, but it was more dulled than it was before. She looked around her body.

And then she panicked again when she saw what it had done to her, part of her mind giving great thanks that there was nopony there to see her doing it.

Then she calmed a little. Just enough to look around at the fact she had been left here to do utterly nothing while the Doctor was doing something important with Puzzlehunt. This was completely ignoring her greatness and power.

So she used her horn to undo the shackles on her hooves. It was tiring work considering she was really drained at the moment. She slowly managed to lift them off and let them fall to the floor. She understood that taking the tube off her mouth would let the disease ravage through her again, but she knew she could hold her own by herself. So she used her magic to lift it out.

For five seconds she felt exactly what a fatal heart attack felt like. Then it passed. She began to cough periodically. Then that passed as well and she collected the energy she had in her. Then she got up and walked out of the room.

Walking seemed to make it feel better somehow. She walked through the corridors and out into the console room. Then she opened the TARDIS doors like she did before and allowed herself to go into a diseased ship to help the Doctor.


	8. Chapter 7: Full Circle

Chapter 7: Full Circle

**=The Carrier 9 Viral Research Vessel, The Disease Processing Laboratory, 3222 C.E. =**

Puzzlehunt caught up to the Doctor, dodging around infected areas of the ship.

"What is it?" The Doctor asked quietly, looking ahead.

"I just considered something. Since I've been up and walking around, I haven't noticed the disease in me at all. Why do you think that is?" Puzzlehunt asked, not whispering at all.

"Well, there is the likelihood that you need to be breathing it in constantly for it to have any effect on you. That only happens when infected ponies breathe it out into the air. Their blood may actually be sterile." The Doctor said, coming to the realization.

"Exactly. I figured that out all by myself. So really, being here is in fact meaningless, as we can fight it off by ourselves. The ponies on this ship are dying **because** they were confined to quarantine." Puzzlehunt said proudly. "By the way, why are you whispering?"

The Doctor pointed ahead. Puzzlehunt looked to see two very mutated infected ponies contorted in the most disgusting way. And they appeared to have not seen them yet (Then again, they didn't know where the eyes were at.)

"Oh." Puzzlehunt said quietly.

And then they snapped their heads at them and began to charge in their direction.

The Doctor and Puzzlehunt quickly found that the mutated ponies were moving at them too quick for them to get out of the way in time.

And then there was a gigantic burst of white light which they were able to duck away from in time.

And when it faded away, the mutants were just more blood on the floor and they were relatively safe.

But the Doctor could still see the white light flickering from an exposed wire nearby. He dodged and jumped around the puddles of blood that were almost covering the floor to get to it. Puzzlehunt decided to stay where he was.

The Doctor jumped right next to the wire and examined it closely. "This is the wires that transport the energy for that sterilization chamber we saw when we first got there." He called over. "They're overloading."

"They're overloading? What does that mean?" Puzzlehunt asked.

"Well, the energy is bursting through the wires due to some malfunction. They make those flashes like the one we saw at exposed wires like this."

"Then do you really think it's a good idea to be standing right next to it?" Puzzlehunt said.

The Doctor considered this for a moment, and then quickly began to make his way back over.

Puzzlehunt rolled his eyes and they began to make their way back. "Boy, the solution really seems to make the whole thing seem completely pointless, huh?"

"That usually happens." The Doctor said. "The solution usually is so simple and makes the situation it solves seem idiotic. Knowing that fighting this disease off is so easy does make all the lengths we've all gone to seem futile. The white stallion seems like an idiot. Everypony on this ship does simply because they leaped right over an answer that was right there."

"So did we." Puzzlehunt pointed out, looking rather embarrassed.

"Yes, exactly. I guess we just leave now. There isn't really anything we can do for the white stallion. He's wrapped himself so far into this that he wouldn't accept it to be so easy. Plus, this ship won't last long, and I know he has every intention of letting himself go down with it." The Doctor explained.

"That's probably true. I think all he's been doing for a while is waiting to die and acting like he's not." Puzzlehunt muttered to himself.

And they hopped around the puddles just for safety.

Meanwhile, Trixie was hobbling through barely 100 feet away from them. But instead of going down one hallway, she went down the other.

She walked down it for a few minutes before she saw that ahead of her the hallway was completely darkened. Then the light above went dead, causing her to jump back. She backed up very far as this continued to happen.

Then she got back into the room with the sterilization chamber as the last light in that hallway flickered off.

She watched as the lights in the hallway nearby that The Doctor and Puzzlehunt were currently in flickered off.

And then the ones that were leading to quarantine all shut down in the same order.

And very last, the ones leading up to the TARDIS.

And now she was standing in the middle of the only room that had light in it. She craned her neck into all the hallways to see that the only light in them were small flickers of white light here and there from very far away.

It was the same in all of them, as she found as she checked. It was rather frightening to be in all that darkness or in the center of it, especially since you couldn't see at all what was in it.

And as she was looking into the hallway she had just been in, the white stallion reached out and grabbed her.

It was sudden enough to nearly make her scream. She gasped multiple times as the white stallion reaffirmed his grip on her to make it completely inescapable.

"I'm turning off everything. All the energy will go into the sterilization of this ship. It will be able to bypass the spells holding it in place. I won't allow you to be off this ship when it happens." He said.

Trixie swallowed as she was dragged over to the control panel for the chamber. She could do nothing but watch him press several levers and turn every knob on the panel. And then he kicked her back. He walked into the chamber and triple locked the door, locking him in completely with no chance of escape. He didn't want to escape.

Then he pulled out a scalpel. He used it to slice open the harness he was wearing. And he pulled it off completely. Trixie was nearly sick at this. There was no skin beneath the harness. The harness itself was fused into his skin and when he cut it off, it revealed only flesh.

And then the only light left on the ship turned off, plunging everything into absolute darkness.

And then Trixie very nearly screamed. She could hear things all around her. The white stallion groaned in pain for a moment, and she could hear the mutants coming out in the distance.

And the most relieving thing she heard was the Doctor yelling, "Come on!" and pulling her into what she hoped was the direction of the TARDIS.

She hoped.

And as she was led through the darkness that was even darker than closing her eyes, hope was really all she had to go on.

They ran a very long distance, as she wondered about whether or not Puzzlehunt was there too, until they ran into the TARDIS console room, where she saw he was.

The Doctor quickly dematerialized the TARDIS. Their escape came as a breath of fresh air. As they knew that behind them, in a flash of white light with the white stallion in the center, the ship they were just on would be gone.

But Trixie was still unhappy. Because as she looked at herself, she knew her cutie mark was still gone.

To be continued in Episode 11.


End file.
